Hi Ory, Piper files are equivalent of the XML descriptor files which helps in adding required analysis engines.
You can manipulate analysis engines for CPE using CPE configurator. Check this link for more info - http://uima.apache.org/downloads/releaseDocs/2.3.0-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#ugr.tug.cpe.configurator_and_viewer Regards, Gandhi From: Ory Henn <[email protected]> Sent: Sunday, August 26, 2018 5:25 PM To: [email protected] Subject: Re: How do I add a dictionary (like NCI) to cTakes lookup? [EXTERNAL] Thanks, Gandhi. I took a look at the module, but am still a bit confused, as the connection between the CPE tool and the piper files is not clear to me. I've succeeded in using my own dictionary with the Default Clinical Pipeline, both through -l argument and through adding a LookupXml parameter in the DefaultFastPipeline.piper script (as in ctakes-rest-service above). But when I run the CPE tool, it still references the default dictionary. My question is - what is the link betwenn CVD/CPE tools and the piper files? Specifically, can I configure the CPE tool to use my piper file, or configure it to use a different lookup? Many thanks, Ory On Thu, Aug 23, 2018 at 8:04 AM, Gandhi Rajan Natarajan <[email protected]<mailto:[email protected]>> wrote: Hi Ory, I suggest you to have a look at this ctakes rest module - https://github.com/GoTeamEpsilon/ctakes-rest-service/tree/master/ctakes-web-rest The custom dictionary XML needs to be placed in ‘resources/org/apache/ctakes/dictionary/lookup/fast’ folder and ‘LookupXml’ attribute needs to be added in DictionarySubPipe.piper as follows: add DefaultJCasTermAnnotator LookupXml=org/apache/ctakes/dictionary/lookup/fast/customDictionary.xml From: Ory Henn <[email protected]<mailto:[email protected]>> Sent: Wednesday, August 22, 2018 8:42 PM To: [email protected]<mailto:[email protected]> Subject: Re: How do I add a dictionary (like NCI) to cTakes lookup? [EXTERNAL] Thanks, Timothy. I fixed the permissions issue and was able to progress further. I am now stuck at the very last step (it would seem), the Dictionary Creator GUI page says this: --- Once a new dictionary has been built, point to it in one of 2 ways: Set the fast dictionary parameter LookupXml to org/apache/ctakes/dictionary/lookup/fast/DictionaryName.xml --- Where is this LookupXml parameter to be found/added? On Wed, Aug 22, 2018 at 4:50 PM, Miller, Timothy <[email protected]<mailto:[email protected]>> wrote: Looks like maybe you don't have permissions to write to that directory (/usr/local/). Can you write it somewhere else? ________________________________ From: Ory Henn <[email protected]<mailto:[email protected]>> Sent: Wednesday, August 22, 2018 9:15 AM To: [email protected]<mailto:[email protected]> Subject: Re: How do I add a dictionary (like NCI) to cTakes lookup? [EXTERNAL] Thanks a lot Ghandi, Michael, for quick and helpful replies. The video especially was very useful, but I'm encountering an error at the last part (building the actual dictionary). It looks like it has a problem with an HsqlDB table (log output below). Can anyone help with this? Do I need to install HsqlDB, or does it come as part of UMLS/Metamorphosys? Thanks, Ory 22 Aug 2018 16:06:40 INFO MrConsoParser - File Lines: 14089874 Concepts: 450236 Texts: 1380174 22 Aug 2018 16:06:40 INFO DictionaryBuilder - Performing Poor man's WSD ... 22 Aug 2018 16:06:42 INFO DictionaryBuilder - Concepts: 446510 Texts: 1162474 22 Aug 2018 16:06:42 INFO DictionaryBuilder - Done Parsing Concepts 22 Aug 2018 16:06:42 INFO JdbcUtil - Connecting to jdbc:hsqldb:file:/usr/local/apache-ctakes-4.0.0/resources/org/apache/ctakes/dictionary/lookup/fast/umls_test_nci/umls_test_nci as SA 22 Aug 2018 16:06:42 INFO ENGINE - Checkpoint start 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose start 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose synched 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose script done 22 Aug 2018 16:06:42 INFO ENGINE - checkpointClose end 22 Aug 2018 16:06:42 INFO ENGINE - Checkpoint end - txts: 1 22 Aug 2018 16:06:43 ERROR RareWordDbWriter - user lacks privilege or object not found: NCI_NCI in statement [insert into nci_nci_hl7 (CUI,NCI_NCI-HL7) values (?,?)] 22 Aug 2018 16:06:43 ERROR MainPanel - Dictionary umls_test_nci could not be built in /usr/local/apache-ctakes-4.0.0 On Mon, Aug 20, 2018 at 10:13 PM, Michael Trepanier <[email protected]<mailto:[email protected]>> wrote: Ory, In response to Gandhi's comments, the video below outlines custom dictionary creation in detail: https://www.youtube.com/watch?v=4aOnafv-NQs<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.youtube.com_watch-3Fv-3D4aOnafv-2DNQs&d=DwMFaQ&c=qS4goWBT7poplM69zy_3xhKwEW14JZMSdioCoppxeFU&r=Heup-IbsIg9Q1TPOylpP9FE4GTK-OqdTDRRNQXipowRLRjx0ibQrHEo8uYx6674h&m=JrSEaNyFWIA-oT8ihZMLVdfYZvdudMkgfc2e13UOvFc&s=A8Md_8ifzCAHha2tRJ_d-kGLk26gNMdOgfpXd3_qKHI&e=> Best, Mike On Mon, Aug 20, 2018 at 2:09 AM, Gandhi Rajan Natarajan <[email protected]<mailto:[email protected]>> wrote: Hi Ory, I guess RxNORM and SNOMED_CT dictionaries are loaded by default. If you want to lookup from other dictionaries like MEDDRA etc. , you may have to create your custom dictionary using cTAKES dictionary generator GUI. That’s what I did to include MEDDRA dictionary terms. -----Original Message----- From: Ory Henn <[email protected]<mailto:[email protected]>> Sent: Monday, August 20, 2018 1:52 PM To: [email protected]<mailto:[email protected]> Cc: Guy Gildor <[email protected]<mailto:[email protected]>> Subject: How do I add a dictionary (like NCI) to cTakes lookup? Hello, New user here (-; I've downloaded and installed cTakes (+UMLS + all resources), and am trying to parse a single document. I see that cTakes (CVD/CPE) identifies CUIs only from RxNORM and SNOMED_CT. 1. What is the way to make cTakes look in more UMLS dictionaries? I specifically need NCI as well. 2. Is there an easy way to make cTakes look in all UMLS dictionaries? 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